Macrophage integrate from inflamed tissue

(weighted PCA, harmony, and SNN)

Fan Zhang

2020-06-04

Only focus on macrophage integration of COVID-19 and other 5 inflammatory disease tissues

Preprocessing

Explore the potential "batch variables"

Correcting sample only

Correcting dataset only

Correcting sample and dataset simultaneously

Correcting for samples for the 10X data, correcting dataset for the AMP data since each donor sample only has less than 100 cells

Visualize UMAP for correcting sample

Visualize UMAP for correcting dataset

Visualize UMAP for correcting dataset and sample simultaneous

Visualize UMAP of correcting for samples for the 10X data, correcting dataset for the AMP data since each donor sample only has less than 100 cells

Compare with original clustering lables

Inflammatory marcorphages from different diseased tissues are clustered together in the integrative embeddings

Build SNN

For weighted clustering, weigh the SNN before passing it to Louvain

Louvain clustering

Identify main shared clusters

Plot some key gene signatures